Strain identifier

BacDive ID: 7857

Type strain: Yes

Species: Catellatospora chokoriensis

Strain Designation: 2-25(1)

Strain history: I. Ara 2-25(1).

NCBI tax ID(s): 310353 (species)

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General

@ref: 12184

BacDive-ID: 7857

DSM-Number: 44900

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Catellatospora chokoriensis 2-25 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sandy soil.

NCBI tax id

  • NCBI tax id: 310353
  • Matching level: species

strain history

@refhistory
12184<- JCM <- I. Ara
67770I. Ara 2-25(1).

doi: 10.13145/bacdive7857.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Catellatospora
  • species: Catellatospora chokoriensis
  • full scientific name: Catellatospora chokoriensis Ara and Kudo 2006

@ref: 12184

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Catellatospora

species: Catellatospora chokoriensis

full scientific name: Catellatospora chokoriensis Ara and Kudo 2006

strain designation: 2-25(1)

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31592positiverod-shapedno
69480no93.632
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
20138Dahlia yellow (1033)10-14 daysISP 2
20138Dahlia yellow (1033)10-14 daysISP 3
20138Dahlia yellow (1033)10-14 daysISP 4
20138Dahlia yellow (1033)10-14 daysISP 5
20138Dahlia yellow (1033)10-14 daysISP 6
20138Dahlia yellow (1033)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20138noISP 2
20138noISP 3
20138noISP 4
20138noISP 5
20138noISP 6
20138noISP 7

pigmentation

  • @ref: 31592
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12184ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
12184YEAST-STARCH-AGAR(B) (DSMZ Medium 656)yeshttps://mediadive.dsmz.de/medium/656Name: YEAST-STARCH-AGAR(B) (DSMZ Medium 656) Composition: Starch 15.0 g/l Agar 15.0 g/l Yeast extract 4.0 g/l MgSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l Distilled water
20138ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20138ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20138ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20138ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20138ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20138ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
12184YEAST STARCH AGAR (A) (DSMZ Medium 1027)yeshttps://mediadive.dsmz.de/medium/1027Name: YEAST STARCH AGAR (A) (DSMZ Medium 1027) Composition: Agar 15.0 g/l Starch 10.0 g/l Yeast extract 2.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
12184positivegrowth28mesophilic
20138positiveoptimum28mesophilic
31592positivegrowth15-30
31592positiveoptimum15-30
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31592positivegrowth06-09alkaliphile
31592positiveoptimum06-09

Physiology and metabolism

oxygen tolerance

  • @ref: 31592
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31592yes
69481yes100
69480yes100

observation

@refobservation
31592aggregates in chains
67770quinones: MK-9(H4), MK-9(H6), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2013817234glucose+
2013822599arabinose+
2013817992sucrose+
2013818222xylose-
2013817268myo-inositol-
2013829864mannitol-
2013828757fructose-
2013826546rhamnose-
2013816634raffinose-
2013862968cellulose+
3159222599arabinose+carbon source
3159228260galactose+carbon source
3159217234glucose+carbon source
3159217306maltose+carbon source
3159237684mannose+carbon source
3159228053melibiose+carbon source
3159217814salicin+carbon source
3159217992sucrose+carbon source
3159227082trehalose+carbon source
3159218222xylose+carbon source

enzymes

@refvalueactivityec
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20138+++-++-++++++-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12184sandy soilChokoria, Cox's BazarBangladeshBGDAsia
67770Sandy soil at a forest-side waterfallChokoria, Cox's BazarBangladeshBGDAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_19076.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_3745;97_11741;98_14429;99_19076&stattab=map
  • Last taxonomy: Catellatospora
  • 16S sequence: AB200231
  • Sequence Identity:
  • Total samples: 1372
  • soil counts: 939
  • aquatic counts: 89
  • animal counts: 57
  • plant counts: 287

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121841Risk group (German classification)
201381German classification

Sequence information

16S sequences

  • @ref: 12184
  • description: Catellatospora chokoriensis gene for 16S rRNA, partial sequence
  • accession: AB200231
  • length: 1481
  • database: ena
  • NCBI tax ID: 310353

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Catellatospora chokoriensis NBRC 107358GCA_016862595contigncbi310353
66792Catellatospora chokoriensis strain NBRC 107358310353.4wgspatric310353
67770Catellatospora chokoriensis 2-25(1)GCA_011297315scaffoldncbi310353

GC content

@refGC-contentmethod
3159271
6777071high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes88.457yes
anaerobicno99.334no
halophileno94.402no
spore-formingyes93.363yes
glucose-utilyes88.062yes
flagellatedno98.137yes
aerobicyes93.229yes
thermophileno98.667yes
motileno93.661yes
glucose-fermentno89.87no

External links

@ref: 12184

culture collection no.: DSM 44900, JCM 12950, NBRC 107358, CGMCC 4.5499, CIP 109162

straininfo link

  • @ref: 77294
  • straininfo: 289971

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16449446Three novel species of the genus Catellatospora, Catellatospora chokoriensis sp. nov., Catellatospora coxensis sp. nov. and Catellatospora bangladeshensis sp. nov., and transfer of Catellatospora citrea subsp. methionotrophica Asano and Kawamoto 1988 to Catellatospora methionotrophica sp. nov., comb. nov.Ara I, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.63862-02006Bacterial Typing Techniques, Bangladesh, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Micromonosporaceae/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny26467683Catellatospora vulcania sp. nov. and Catellatospora paridis sp. nov., two novel actinobacteria isolated from volcanic sediment and the rhizosphere of Paris polyphylla.Jia F, Guo S, Shen Y, Gao M, Liu C, Zhou S, Li J, Guan X, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-015-0608-y2015Base Sequence, China, Cluster Analysis, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Geologic Sediments/*microbiology, Micromonosporaceae/chemistry/*classification/genetics/*isolation & purification, Microscopy, Electron, Scanning, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Tracheophyta/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12184Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44900)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44900
20138Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44900.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31592Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2788128776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77294Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289971.1StrainInfo: A central database for resolving microbial strain identifiers